--- /srv/rebuilderd/tmp/rebuilderdSQBMUi/inputs/r-bioc-fishpond_2.18.0+ds-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdSQBMUi/out/r-bioc-fishpond_2.18.0+ds-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-12 00:44:43.000000 debian-binary │ --rw-r--r-- 0 0 0 2076 2026-08-12 00:44:43.000000 control.tar.xz │ --rw-r--r-- 0 0 0 372764 2026-08-12 00:44:43.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1940 2026-08-12 00:44:43.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 372796 2026-08-12 00:44:43.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1245 2026-08-12 00:44:43.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 3497 2026-08-12 00:44:43.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 953 2026-08-12 00:44:43.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 3413 2026-08-12 00:44:43.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,13 @@ │ │ │ Package: r-bioc-fishpond │ │ │ Version: 2.18.0+ds-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 507 │ │ │ +Installed-Size: 506 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-cran-abind, r-cran-gtools, r-bioc-qvalue, r-bioc-s4vectors, r-bioc-iranges, r-bioc-summarizedexperiment, r-bioc-genomicranges, r-cran-matrixstats, r-cran-svmisc, r-cran-matrix, r-bioc-singlecellexperiment, r-cran-jsonlite, r-pkg-team-core-architecture │ │ │ -Suggests: r-cran-testthat, r-cran-knitr, r-cran-rmarkdown, r-bioc-tximeta, r-bioc-org.hs.eg.db, r-cran-samr, r-bioc-deseq2, r-bioc-tximportdata, r-bioc-limma, r-bioc-ensembldb, r-bioc-genomicfeatures, r-bioc-annotationdbi, r-cran-pheatmap, r-bioc-gviz, r-bioc-genomeinfodb, r-cran-data.table │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/fishpond/ │ │ │ Description: Differential transcript and gene expression with inferential replicates │ │ │ Fishpond contains methods for differential transcript │ │ │ and gene expression analysis of RNA-seq data using inferential │ │ │ replicates for uncertainty of abundance quantification, │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -3,15 +3,14 @@ │ │ │ │ usr/lib/R/site-library/fishpond/INDEX │ │ │ │ usr/lib/R/site-library/fishpond/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/fishpond/Meta/features.rds │ │ │ │ usr/lib/R/site-library/fishpond/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/fishpond/Meta/links.rds │ │ │ │ usr/lib/R/site-library/fishpond/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/fishpond/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/fishpond/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/fishpond/NAMESPACE │ │ │ │ usr/lib/R/site-library/fishpond/NEWS.md │ │ │ │ usr/lib/R/site-library/fishpond/R/fishpond │ │ │ │ usr/lib/R/site-library/fishpond/R/fishpond.rdb │ │ │ │ usr/lib/R/site-library/fishpond/R/fishpond.rdx │ │ │ │ usr/lib/R/site-library/fishpond/README.md │ │ │ │ usr/lib/R/site-library/fishpond/doc/allelic.R ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -10,26 +10,25 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1202 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1119 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 437 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 970 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1933 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 284 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2700 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 12191 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/NEWS.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/R/fishpond │ │ │ --rw-r--r-- 0 root (0) root (0) 146295 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/R/fishpond.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1200 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/R/fishpond.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 146305 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/R/fishpond.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1195 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/R/fishpond.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 2836 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 10790 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/doc/allelic.R │ │ │ -rw-r--r-- 0 root (0) root (0) 23592 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/doc/allelic.Rmd │ │ │ --rw-r--r-- 0 root (0) root (0) 2091 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 1387 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 15625 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/doc/swish.R │ │ │ -rw-r--r-- 0 root (0) root (0) 43398 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/doc/swish.Rmd │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/extdata/ │ │ │ -rw-r--r-- 0 root (0) root (0) 512 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/extdata/Snakefile │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/extdata/alevin/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/extdata/alevin/example-quants/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/extdata/alevin/example-quants/fry-usa-basic/ │ │ │ @@ -42,17 +41,17 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1322 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/extdata/animation-code.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 554 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 294 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/aliases.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/figures/ │ │ │ -rw-r--r-- 0 root (0) root (0) 98798 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/figures/fishpond.png │ │ │ -rw-r--r-- 0 root (0) root (0) 16966 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/figures/plotInfReps.png │ │ │ --rw-r--r-- 0 root (0) root (0) 70251 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/fishpond.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 694 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/fishpond.rdx │ │ │ --rw-r--r-- 0 root (0) root (0) 358 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 70739 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/fishpond.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 691 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/fishpond.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 369 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 4372 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/script/ │ │ │ -rw-r--r-- 0 root (0) root (0) 610 2026-08-12 00:44:43.000000 ./usr/lib/R/site-library/fishpond/script/timing.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:44:43.000000 ./usr/share/doc/ │ │ ├── ./usr/lib/R/site-library/fishpond/R/fishpond.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -35,15 +35,15 @@ │ │ │ │ "imports" = " stats = c(quantile = "quantile"), stats = c(rnbinom = "rnbinom"), " │ │ │ │ "imports" = " stats = c(rpois = "rpois"), stats = c(runif = "runif"), stats = c(var = "var"), " │ │ │ │ "imports" = " svMisc = c(progress = "progress"), utils = c(capture.output = "capture.output"), " │ │ │ │ "imports" = " utils = c(head = "head"), utils = c(read.csv = "read.csv"), " │ │ │ │ "imports" = " utils = c(read.table = "read.table"), utils = c(tail = "tail"), " │ │ │ │ "imports" = " utils = c(write.table = "write.table"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-fishpond/debian/r-bioc-fishpond/usr/lib/R/site-library/fishpond"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/debian/r-bioc-fishpond/usr/lib/R/site-library/fishpond"" │ │ │ │ "spec" = "c(name = "fishpond", version = "2.18.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/fishpond/R/fishpond.rdx │ │ │ ├── fishpond.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,214 +1,214 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 1401 52 │ │ │ │ │ +[1] 1411 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 1584 52 │ │ │ │ │ +[1] 1594 52 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 1636 53 │ │ │ │ │ +[1] 1646 53 │ │ │ │ │ │ │ │ │ │ $variables$addStatsFromCSV │ │ │ │ │ -[1] 1689 1448 │ │ │ │ │ +[1] 1699 1448 │ │ │ │ │ │ │ │ │ │ $variables$alevinEC │ │ │ │ │ -[1] 3137 4863 │ │ │ │ │ +[1] 3147 4863 │ │ │ │ │ │ │ │ │ │ $variables$boxplot2 │ │ │ │ │ -[1] 8000 1572 │ │ │ │ │ +[1] 8010 1572 │ │ │ │ │ │ │ │ │ │ $variables$checkPair │ │ │ │ │ -[1] 9572 751 │ │ │ │ │ +[1] 9582 751 │ │ │ │ │ │ │ │ │ │ $variables$computeInfRV │ │ │ │ │ -[1] 10323 1943 │ │ │ │ │ +[1] 10333 1943 │ │ │ │ │ │ │ │ │ │ $variables$deswish │ │ │ │ │ -[1] 12266 2676 │ │ │ │ │ +[1] 12276 2676 │ │ │ │ │ │ │ │ │ │ $variables$estimatePi0 │ │ │ │ │ -[1] 14942 553 │ │ │ │ │ +[1] 14952 553 │ │ │ │ │ │ │ │ │ │ $variables$getCorStat │ │ │ │ │ -[1] 15495 1922 │ │ │ │ │ +[1] 15505 1922 │ │ │ │ │ │ │ │ │ │ $variables$getDeltaLFC │ │ │ │ │ -[1] 17417 773 │ │ │ │ │ +[1] 17427 773 │ │ │ │ │ │ │ │ │ │ $variables$getInfReps │ │ │ │ │ -[1] 18190 567 │ │ │ │ │ +[1] 18200 567 │ │ │ │ │ │ │ │ │ │ $variables$getInterxPairStat │ │ │ │ │ -[1] 18757 1071 │ │ │ │ │ +[1] 18767 1071 │ │ │ │ │ │ │ │ │ │ $variables$getLog2FC │ │ │ │ │ -[1] 19828 1151 │ │ │ │ │ +[1] 19838 1151 │ │ │ │ │ │ │ │ │ │ $variables$getLog2FCNumX │ │ │ │ │ -[1] 20979 1190 │ │ │ │ │ +[1] 20989 1190 │ │ │ │ │ │ │ │ │ │ $variables$getLog2FCPair │ │ │ │ │ -[1] 22169 1067 │ │ │ │ │ +[1] 22179 1067 │ │ │ │ │ │ │ │ │ │ $variables$getPairPerms │ │ │ │ │ -[1] 23236 2106 │ │ │ │ │ +[1] 23246 2106 │ │ │ │ │ │ │ │ │ │ $variables$getPerms │ │ │ │ │ -[1] 25342 1108 │ │ │ │ │ +[1] 25352 1108 │ │ │ │ │ │ │ │ │ │ $variables$getPseudoPair │ │ │ │ │ -[1] 26450 1102 │ │ │ │ │ +[1] 26460 1102 │ │ │ │ │ │ │ │ │ │ $variables$getSamStat │ │ │ │ │ -[1] 27552 1807 │ │ │ │ │ +[1] 27562 1807 │ │ │ │ │ │ │ │ │ │ $variables$getSignedRank │ │ │ │ │ -[1] 29359 1507 │ │ │ │ │ +[1] 29369 1507 │ │ │ │ │ │ │ │ │ │ $variables$getTrace │ │ │ │ │ -[1] 30866 1753 │ │ │ │ │ +[1] 30876 1753 │ │ │ │ │ │ │ │ │ │ $variables$getZscore │ │ │ │ │ -[1] 32619 1042 │ │ │ │ │ +[1] 32629 1042 │ │ │ │ │ │ │ │ │ │ $variables$grSelect │ │ │ │ │ -[1] 33661 507 │ │ │ │ │ +[1] 33671 507 │ │ │ │ │ │ │ │ │ │ $variables$importAllelicCounts │ │ │ │ │ -[1] 34168 7768 │ │ │ │ │ +[1] 34178 7768 │ │ │ │ │ │ │ │ │ │ $variables$infRepError │ │ │ │ │ -[1] 41936 397 │ │ │ │ │ +[1] 41946 397 │ │ │ │ │ │ │ │ │ │ $variables$isoformProportions │ │ │ │ │ -[1] 42333 2923 │ │ │ │ │ +[1] 42343 2923 │ │ │ │ │ │ │ │ │ │ $variables$joinNearbyTss │ │ │ │ │ -[1] 45256 504 │ │ │ │ │ +[1] 45266 504 │ │ │ │ │ │ │ │ │ │ $variables$labelKeep │ │ │ │ │ -[1] 45760 1634 │ │ │ │ │ +[1] 45770 1634 │ │ │ │ │ │ │ │ │ │ $variables$loadFry │ │ │ │ │ -[1] 47394 5503 │ │ │ │ │ +[1] 47404 5503 │ │ │ │ │ │ │ │ │ │ $variables$load_fry_raw │ │ │ │ │ -[1] 52897 2401 │ │ │ │ │ +[1] 52907 2401 │ │ │ │ │ │ │ │ │ │ $variables$makeInfReps │ │ │ │ │ -[1] 55298 2132 │ │ │ │ │ +[1] 55308 2132 │ │ │ │ │ │ │ │ │ │ $variables$makeIsoProp │ │ │ │ │ -[1] 57430 713 │ │ │ │ │ +[1] 57440 713 │ │ │ │ │ │ │ │ │ │ $variables$makeLocFDR │ │ │ │ │ -[1] 58143 1083 │ │ │ │ │ +[1] 58153 1083 │ │ │ │ │ │ │ │ │ │ $variables$makeQvalue │ │ │ │ │ -[1] 59226 1417 │ │ │ │ │ +[1] 59236 1417 │ │ │ │ │ │ │ │ │ │ $variables$makeSamrObj │ │ │ │ │ -[1] 60643 633 │ │ │ │ │ +[1] 60653 633 │ │ │ │ │ │ │ │ │ │ $variables$makeSimSwishData │ │ │ │ │ -[1] 61276 6406 │ │ │ │ │ +[1] 61286 6406 │ │ │ │ │ │ │ │ │ │ $variables$makeTx2Tss │ │ │ │ │ -[1] 67682 3038 │ │ │ │ │ +[1] 67692 3038 │ │ │ │ │ │ │ │ │ │ $variables$medianOverMean │ │ │ │ │ -[1] 70720 372 │ │ │ │ │ +[1] 70730 372 │ │ │ │ │ │ │ │ │ │ $variables$miniSwish │ │ │ │ │ -[1] 71092 1686 │ │ │ │ │ +[1] 71102 1686 │ │ │ │ │ │ │ │ │ │ $variables$my_as_dgcmatrix │ │ │ │ │ -[1] 72778 302 │ │ │ │ │ +[1] 72788 302 │ │ │ │ │ │ │ │ │ │ $variables$permsNote │ │ │ │ │ -[1] 73080 484 │ │ │ │ │ +[1] 73090 484 │ │ │ │ │ │ │ │ │ │ $variables$plotAllelicGene │ │ │ │ │ -[1] 73564 11473 │ │ │ │ │ +[1] 73574 11473 │ │ │ │ │ │ │ │ │ │ $variables$plotAllelicHeatmap │ │ │ │ │ -[1] 85037 2177 │ │ │ │ │ +[1] 85047 2177 │ │ │ │ │ │ │ │ │ │ $variables$plotInfReps │ │ │ │ │ -[1] 87214 9985 │ │ │ │ │ +[1] 87224 9985 │ │ │ │ │ │ │ │ │ │ $variables$plotMASwish │ │ │ │ │ -[1] 97199 924 │ │ │ │ │ +[1] 97209 924 │ │ │ │ │ │ │ │ │ │ $variables$postprocess │ │ │ │ │ -[1] 98123 856 │ │ │ │ │ +[1] 98133 856 │ │ │ │ │ │ │ │ │ │ $variables$randomSamplesToRemove │ │ │ │ │ -[1] 98979 1284 │ │ │ │ │ +[1] 98989 1284 │ │ │ │ │ │ │ │ │ │ $variables$readBFH │ │ │ │ │ -[1] 100263 3255 │ │ │ │ │ +[1] 100273 3255 │ │ │ │ │ │ │ │ │ │ $variables$readEq │ │ │ │ │ -[1] 103518 1841 │ │ │ │ │ +[1] 103528 1841 │ │ │ │ │ │ │ │ │ │ $variables$readExampleFryData │ │ │ │ │ -[1] 105359 1510 │ │ │ │ │ +[1] 105369 1510 │ │ │ │ │ │ │ │ │ │ $variables$salmonEC │ │ │ │ │ -[1] 106869 4679 │ │ │ │ │ +[1] 106879 4679 │ │ │ │ │ │ │ │ │ │ $variables$scaleInfReps │ │ │ │ │ -[1] 111548 4399 │ │ │ │ │ +[1] 111558 4399 │ │ │ │ │ │ │ │ │ │ $variables$splitSwish │ │ │ │ │ -[1] 115947 2157 │ │ │ │ │ +[1] 115957 2157 │ │ │ │ │ │ │ │ │ │ $variables$sv.cbind │ │ │ │ │ -[1] 118104 1059 │ │ │ │ │ +[1] 118114 1059 │ │ │ │ │ │ │ │ │ │ $variables$swish │ │ │ │ │ -[1] 119163 6548 │ │ │ │ │ +[1] 119173 6548 │ │ │ │ │ │ │ │ │ │ $variables$swishCor │ │ │ │ │ -[1] 125711 1633 │ │ │ │ │ +[1] 125721 1633 │ │ │ │ │ │ │ │ │ │ $variables$swishCorPair │ │ │ │ │ -[1] 127344 3204 │ │ │ │ │ +[1] 127354 3204 │ │ │ │ │ │ │ │ │ │ $variables$swishInterx │ │ │ │ │ -[1] 130548 3057 │ │ │ │ │ +[1] 130558 3057 │ │ │ │ │ │ │ │ │ │ $variables$swishInterxPair │ │ │ │ │ -[1] 133605 2995 │ │ │ │ │ +[1] 133615 2995 │ │ │ │ │ │ │ │ │ │ $variables$swishPair │ │ │ │ │ -[1] 136600 2490 │ │ │ │ │ +[1] 136610 2490 │ │ │ │ │ │ │ │ │ │ $variables$swishStrat │ │ │ │ │ -[1] 139090 3052 │ │ │ │ │ +[1] 139100 3052 │ │ │ │ │ │ │ │ │ │ $variables$swishTwoGroup │ │ │ │ │ -[1] 142142 1601 │ │ │ │ │ +[1] 142152 1601 │ │ │ │ │ │ │ │ │ │ $variables$writeExampleFryDat │ │ │ │ │ -[1] 143743 2552 │ │ │ │ │ +[1] 143753 2552 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 291 1110 │ │ │ │ │ +[1] 291 1120 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 160 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 1453 131 │ │ │ │ │ +[1] 1463 131 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/fishpond/doc/index.html │ │ │ @@ -10,34 +10,19 @@ │ │ │ │ │ │
│ │ │
│ │ │ [Up] │ │ │ [Top] │ │ │
│ │ │

Vignettes from package 'fishpond'

│ │ │ - │ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
fishpond::2. SEESAW - Allelic expression analysis with Salmon and Swishsource
fishpond::1. Swish: DE analysis accounting for inferential uncertaintysource
│ │ │ +The package contains no vignette meta-information. │ │ │

Other files in the doc directory

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ │ │ │ + │ │ │
allelic.R
allelic.Rmd
swish.R
swish.Rmd
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,11 +1,10 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''ffiisshhppoonndd'' ********** │ │ │ │ -_f_i_s_h_p_o_n_d_:_: 2. SEESAW - Allelic expression analysis with Salmon and _s_o_u_r_c_e │ │ │ │ - Swish │ │ │ │ -_f_i_s_h_p_o_n_d_:_: 1. Swish: DE analysis accounting for inferential _s_o_u_r_c_e │ │ │ │ - uncertainty │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ ********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ _a_l_l_e_l_i_c_._R │ │ │ │ + _a_l_l_e_l_i_c_._R_m_d │ │ │ │ _s_w_i_s_h_._R │ │ │ │ + _s_w_i_s_h_._R_m_d │ │ ├── ./usr/lib/R/site-library/fishpond/help/fishpond.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -21,15 +21,15 @@ │ │ │ │ structure(list(list(structure("estPi0", Rd_tag = "TEXT")), │ │ │ │ list(structure("logical, see ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("swish", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("the SummarizedExperiment with metadata columns added,\n", Rd_tag = "TEXT"), │ │ │ │ structure("or if ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("y", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ - structure(" is NULL, a data.frame of compiled results\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/addStatsFromCSV.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" is NULL, a data.frame of compiled results\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/addStatsFromCSV.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ alevinEC (list) = structure(list(structure(list(structure("Construct a sparse matrix of transcript compatibility counts from alevin \n", Rd_tag = "TEXT"), │ │ │ │ structure("output", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("alevinEC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("alevinEC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Constructs a UMI count matrix with equivalence class identifiers\n", Rd_tag = "TEXT"), │ │ │ │ @@ -80,15 +80,15 @@ │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("The resulting count matrix uses equivalence class identifiers as rownames.\n", Rd_tag = "TEXT"), │ │ │ │ structure("These can be linked to respective transcripts and genes using the \n", Rd_tag = "TEXT"), │ │ │ │ structure("`tx2gene_matched` element of the output. Specifically, if the equivalence \n", Rd_tag = "TEXT"), │ │ │ │ structure("class identifier reads 1|2|8, then the equivalence class is compatible with\n", Rd_tag = "TEXT"), │ │ │ │ structure("the transcripts and their respective genes in rows 1, 2 and 8 of \n", Rd_tag = "TEXT"), │ │ │ │ structure("`tx2gene_matched`.\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Jeroen Gilis\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/alevinEC.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Jeroen Gilis\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/alevinEC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ computeInfRV (list) = structure(list(structure(list(structure("Compute inferential relative variance (InfRV)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("computeInfRV", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("computeInfRV", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("InfRV", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -144,15 +144,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a SummarizedExperiment with ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("meanInfRV", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" in the metadata columns\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Anqi Zhu, Avi Srivastava, Joseph G Ibrahim, Rob Patro, Michael I Love\n", Rd_tag = "TEXT"), │ │ │ │ structure("\"Nonparametric expression analysis using inferential replicate counts\"\n", Rd_tag = "TEXT"), │ │ │ │ structure("Nucleic Acids Research (2019). ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://doi.org/10.1093/nar/gkz622", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/computeInfRV.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/computeInfRV.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ deswish (list) = structure(list(structure(list(structure("deswish: DESeq2-apeglm With Inferential Samples Helps", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("deswish", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("deswish", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The DESeq2-apeglm With Inferential Samples implementation supposes\n", Rd_tag = "TEXT"), │ │ │ │ structure("a hierarchical distribution of log2 fold changes.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -198,15 +198,15 @@ │ │ │ │ structure("removing the noise and preserving large differences\" Bioinformatics (2018).\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Love, Huber, Anders \"Moderated estimation of fold change and dispersion\n", Rd_tag = "TEXT"), │ │ │ │ structure("for RNA-seq data with DESeq2\" Genome Biology (2014).\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# a small example... 500 genes, 10 inf reps\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- makeSimSwishData(m=500, numReps=10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- labelKeep(y)\n", Rd_tag = "RCODE"), structure("#y <- deswish(y, ~condition, \"condition_2_vs_1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/deswish.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/deswish.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fishpond-package (list) = structure(list(structure(list(structure("Fishpond: downstream methods and tools for expression data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fishpond-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fishpond-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("package", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This package provides statistical methods and other tools for\n", Rd_tag = "TEXT"), │ │ │ │ @@ -248,15 +248,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Compression, makeInfReps and splitSwish:\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Van Buren, S., Sarkar, H., Srivastava, A., Rashid, N.U.,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Patro, R., Love, M.I. (2020)\n", Rd_tag = "TEXT"), │ │ │ │ structure("Compression of quantification uncertainty for scRNA-seq counts.\n", Rd_tag = "TEXT"), │ │ │ │ structure("bioRxiv.\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("https://doi.org/10.1101/2020.07.06.189639", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/fishpond-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/fishpond-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getTrace (list) = structure(list(structure(list(structure("Obtain a trace of inferential replicates for a sample", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getTrace", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getTrace", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Simple helper function to obtain a trace (e.g. MCMC trace)\n", Rd_tag = "TEXT"), │ │ │ │ structure("of the ordered inferential replicates for one samples.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -283,15 +283,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a data.frame with the counts along the interential\n", Rd_tag = "TEXT"), │ │ │ │ structure("replicates, possible with additional columns specifying\n", Rd_tag = "TEXT"), │ │ │ │ structure("feature or sample\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- makeSimSwishData()\n", Rd_tag = "RCODE"), │ │ │ │ structure("getTrace(y, \"gene-1\", \"s1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/getTrace.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/getTrace.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ importAllelicCounts (list) = structure(list(structure(list(structure("Import allelic counts as a SummarizedExperiment", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("importAllelicCounts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("importAllelicCounts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -443,15 +443,15 @@ │ │ │ │ structure(", \n", Rd_tag = "TEXT"), structure("such that comparisons by default will be a1 vs a2\n", Rd_tag = "TEXT"), │ │ │ │ structure("(effect vs non-effect).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Euphy Wu, Noor P. Singh, Kwangbom Choi, Mohsen Zakeri, Matthew\n", Rd_tag = "TEXT"), │ │ │ │ structure("Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Michael I. Love.\n", Rd_tag = "TEXT"), structure("\"Detecting isoform-level allelic imbalance accounting for\n", Rd_tag = "TEXT"), │ │ │ │ structure("inferential uncertainty\" bioRxiv (2022)\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://doi.org/10.1101/2022.08.12.503785", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/importAllelicCounts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/importAllelicCounts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ isoformProportions (list) = structure(list(structure(list(structure("Create isoform proportions from scaled data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("isoformProportions", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("isoformProportions", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Takes output of scaled (and optionally filtered) counts\n", Rd_tag = "TEXT"), │ │ │ │ structure("and returns isoform proportions by dividing out the\n", Rd_tag = "TEXT"), │ │ │ │ @@ -474,15 +474,15 @@ │ │ │ │ structure(list(structure("y", Rd_tag = "RCODE")), Rd_tag = "\\code"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("quiet", Rd_tag = "TEXT")), │ │ │ │ list(structure("display no messages", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a SummarizedExperiment, with single-isoform\n", Rd_tag = "TEXT"), │ │ │ │ structure("transcripts removed, and transcripts now ordered by\n", Rd_tag = "TEXT"), │ │ │ │ - structure("gene\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/isoformProportions.Rd", class = "Rd", meta = list( │ │ │ │ + structure("gene\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/isoformProportions.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ labelKeep (list) = structure(list(structure(list(structure("Label rows to keep based on minimal count", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("labelKeep", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("labelKeep", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Adds a column ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("keep", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -519,15 +519,15 @@ │ │ │ │ structure(list(structure("keep", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("in ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("mcols(y)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- makeSimSwishData()\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- scaleInfReps(y)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("y <- labelKeep(y)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/labelKeep.Rd", class = "Rd", meta = list( │ │ │ │ + structure("y <- labelKeep(y)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/labelKeep.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ loadFry (list) = structure(list(structure(list(structure("Load in data from alevin-fry USA mode", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("loadFry", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("loadFry", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Enables easy loading of sparse data matrices provided by\n", Rd_tag = "TEXT"), │ │ │ │ structure("alevin-fry USA mode.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -690,15 +690,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Load alevin-fry gene quantification in velocity format\n", Rd_tag = "RCODE"), │ │ │ │ structure("sce <- loadFry(fryDir=testdat$parent_dir, outputFormat=custom_velocity_format)\n", Rd_tag = "RCODE"), │ │ │ │ structure("SummarizedExperiment::assayNames(sce)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Load the same data but use pre-defined, velociraptor R pckage desired format\n", Rd_tag = "RCODE"), │ │ │ │ structure("scvelo_format <- \"scVelo\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("scev <- loadFry(fryDir=testdat$parent_dir, outputFormat=scvelo_format, nonzero=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("SummarizedExperiment::assayNames(scev)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/loadFry.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/loadFry.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ makeInfReps (list) = structure(list(structure(list(structure("Make pseudo-inferential replicates from mean and variance", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("makeInfReps", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("makeInfReps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Makes pseudo-inferential replicate counts from\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("mean", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -741,15 +741,15 @@ │ │ │ │ structure("https://doi.org/10.1101/2020.07.06.189639", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(SummarizedExperiment)\n", Rd_tag = "RCODE"), │ │ │ │ structure("mean <- matrix(1:4,ncol=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("variance <- mean\n", Rd_tag = "RCODE"), structure("se <- SummarizedExperiment(list(mean=mean, variance=variance))\n", Rd_tag = "RCODE"), │ │ │ │ structure("se <- makeInfReps(se, numReps=50)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/makeInfReps.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/makeInfReps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ makeSimSwishData (list) = structure(list(structure(list(structure("Make simulated data for swish for examples/testing", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("makeSimSwishData", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("makeSimSwishData", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Makes a small swish dataset for examples and testing.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The first six genes have some differential expression\n", Rd_tag = "TEXT"), │ │ │ │ @@ -791,15 +791,15 @@ │ │ │ │ structure(list(list(structure("dynamicAI", Rd_tag = "TEXT")), │ │ │ │ list(structure("logical, whether to make a dynamic allelic sim dataset", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a SummarizedExperiment\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(SummarizedExperiment)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- makeSimSwishData()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("assayNames(y)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/makeSimSwishData.Rd", class = "Rd", meta = list( │ │ │ │ + structure("assayNames(y)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/makeSimSwishData.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ makeTx2Tss (list) = structure(list(structure(list(structure("Make a GRanges linking transcripts to TSS within gene", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("makeTx2Tss", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("makeTx2Tss", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This helper function takes either a TxDb/EnsDb or\n", Rd_tag = "TEXT"), │ │ │ │ structure("GRanges object as input and outputs a GRanges object\n", Rd_tag = "TEXT"), │ │ │ │ @@ -826,15 +826,15 @@ │ │ │ │ structure(", and\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("group_id", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("library(EnsDb.Hsapiens.v86)\n", Rd_tag = "VERB"), │ │ │ │ structure("edb <- EnsDb.Hsapiens.v86\n", Rd_tag = "VERB"), │ │ │ │ structure("t2t <- makeTx2Tss(edb)\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/makeTx2Tss.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/makeTx2Tss.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ miniSwish (list) = structure(list(structure(list(structure("Helper function for distributing Swish on a subset of data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("miniSwish", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("miniSwish", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function is called by the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Snakefile", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -875,15 +875,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Note that the default for length correction is FALSE, as\n", Rd_tag = "TEXT"), │ │ │ │ structure("opposed to the default in ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("scaleInfReps", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" which\n", Rd_tag = "TEXT"), structure("is TRUE. The default for ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("numReps", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" here is 20.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("nothing, files are written out\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/miniSwish.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("nothing, files are written out\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/miniSwish.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotAllelicGene (list) = structure(list(structure(list(structure("Plot allelic counts in a gene context using Gviz", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotAllelicGene", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotAllelicGene", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot allelic data (allelic proportions, isoform propostions)\n", Rd_tag = "TEXT"), │ │ │ │ structure("in a gene context leveraging the Gviz package. See the allelic\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1054,15 +1054,15 @@ │ │ │ │ structure("This function makes use of the Gviz package that is described in:\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Hahne, F., Ivanek, R. (2016). Visualizing Genomic Data\n", Rd_tag = "TEXT"), │ │ │ │ structure("Using Gviz and Bioconductor.\n", Rd_tag = "TEXT"), │ │ │ │ structure("In: Mathé, E., Davis, S. (eds) Statistical Genomics.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Methods in Molecular Biology, vol 1418. Humana Press,\n", Rd_tag = "TEXT"), │ │ │ │ structure("New York, NY. ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("https://doi.org/10.1007/978-1-4939-3578-9_16", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/plotAllelicGene.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotAllelicGene.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotAllelicHeatmap (list) = structure(list(structure(list(structure("Plot allelic ratio heatmap", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotAllelicHeatmap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotAllelicHeatmap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot allelic ratio heatmap over features and samples\n", Rd_tag = "TEXT"), │ │ │ │ structure("using the pheatmap package. The a1/(a2 + a1) ratio\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1105,15 +1105,15 @@ │ │ │ │ structure("Vincent, Gary A. Churchill, Cheryl L. Ackert-Bicknell, Rob Patro,\n", Rd_tag = "TEXT"), │ │ │ │ structure("Michael I. Love.\n", Rd_tag = "TEXT"), structure("\"Detecting isoform-level allelic imbalance accounting for\n", Rd_tag = "TEXT"), │ │ │ │ structure("inferential uncertainty\" bioRxiv (2022)\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://doi.org/10.1101/2022.08.12.503785", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("This function makes use of the pheatmap package:\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Kolde, Raivo. \"Pheatmap: pretty heatmaps.\"\n", Rd_tag = "TEXT"), │ │ │ │ - structure("R package version 1.2 (2012): 726.\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/plotAllelicHeatmap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("R package version 1.2 (2012): 726.\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotAllelicHeatmap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotInfReps (list) = structure(list(structure(list(structure("Plot inferential replicates for a gene or transcript", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotInfReps", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotInfReps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("For datasets with inferential replicates, boxplots are\n", Rd_tag = "TEXT"), │ │ │ │ structure("drawn for the two groups and potentially grouped by\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1257,15 +1257,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("nothing, a plot is displayed\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- makeSimSwishData()\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotInfReps(y, 3, \"condition\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("y <- makeSimSwishData(n=40)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y$batch <- factor(rep(c(1,2,3,1,2,3),c(5,10,5,5,10,5)))\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotInfReps(y, 3, \"condition\", \"batch\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/plotInfReps.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotInfReps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotMASwish (list) = structure(list(structure(list(structure("MA plot - log fold change over average counts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotMASwish", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotMASwish", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("MA plot - log fold change over average counts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plotMASwish(y, alpha = 0.05, sigcolor = \"blue\", ...)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1284,15 +1284,15 @@ │ │ │ │ list(structure("passed to plot", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("nothing, a plot is displayed\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- makeSimSwishData()\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- scaleInfReps(y)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- labelKeep(y)\n", Rd_tag = "RCODE"), structure("y <- swish(y, x=\"condition\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plotMASwish(y)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/plotMASwish.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plotMASwish(y)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotMASwish.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -1352,15 +1352,15 @@ │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("The resulting count matrix uses equivalence class identifiers as rownames.\n", Rd_tag = "TEXT"), │ │ │ │ structure("These can be linked to respective transcripts and genes using the \n", Rd_tag = "TEXT"), │ │ │ │ structure("`tx2gene_matched` element of the output. Specifically, if the equivalence \n", Rd_tag = "TEXT"), │ │ │ │ structure("class identifier reads 1|2|8, then the equivalence class is compatible with\n", Rd_tag = "TEXT"), │ │ │ │ structure("the transcripts and their respective genes in rows 1, 2 and 8 of \n", Rd_tag = "TEXT"), │ │ │ │ structure("`tx2gene_matched`.\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Jeroen Gilis\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/salmonEC.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Jeroen Gilis\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/salmonEC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ scaleInfReps (list) = structure(list(structure(list(structure("Scale inferential replicate counts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("scaleInfReps", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("scaleInfReps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A helper function to scale the inferential replicates\n", Rd_tag = "TEXT"), │ │ │ │ structure("to the mean sequencing depth. The scaling takes into account\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1421,15 +1421,15 @@ │ │ │ │ structure(list(structure("log10mean", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is also added which is the\n", Rd_tag = "TEXT"), │ │ │ │ structure("log10 of the mean of scaled counts across all samples and all inferential\n", Rd_tag = "TEXT"), │ │ │ │ structure("replicates.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- makeSimSwishData()\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- scaleInfReps(y)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/scaleInfReps.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/scaleInfReps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ splitSwish (list) = structure(list(structure(list(structure("Function for splitting SummarizedExperiment into separate RDS files", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("splitSwish", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("splitSwish", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("splitSwish", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -1490,15 +1490,15 @@ │ │ │ │ structure("https://doi.org/10.1101/2020.07.06.189639", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Snakemake:\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Koster, J., Rahmann, S. (2012)\n", Rd_tag = "TEXT"), │ │ │ │ structure("Snakemake - a scalable bioinformatics workflow engine.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Bioinformatics.\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("https://doi.org/10.1093/bioinformatics/bts480", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/splitSwish.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/splitSwish.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ swish (list) = structure(list(structure(list(structure("Swish method: differential expression accounting for inferential uncertainty", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("swish", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("swish", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The Swish method, or \"SAMseq With Inferential Samples Helps\".\n", Rd_tag = "TEXT"), │ │ │ │ structure("Performs non-parametric inference on rows of ", Rd_tag = "TEXT"), │ │ │ │ @@ -1708,10 +1708,10 @@ │ │ │ │ structure(" mcols(y)$stat[i], 10,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" col=cols[i], length=.1, lwd=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# plot inferential replicates\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotInfReps(y, 1, \"condition\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotInfReps(y, 3, \"condition\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotInfReps(y, 5, \"condition\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-fishpond/man/swish.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/swish.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/fishpond/help/fishpond.rdx │ │ │ ├── fishpond.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,139 +1,139 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$addStatsFromCSV │ │ │ │ │ -[1] 286 1403 │ │ │ │ │ +[1] 295 1417 │ │ │ │ │ │ │ │ │ │ $variables$alevinEC │ │ │ │ │ -[1] 1967 2433 │ │ │ │ │ +[1] 2002 2443 │ │ │ │ │ │ │ │ │ │ $variables$computeInfRV │ │ │ │ │ -[1] 4682 2726 │ │ │ │ │ +[1] 4738 2739 │ │ │ │ │ │ │ │ │ │ $variables$deswish │ │ │ │ │ -[1] 7686 2336 │ │ │ │ │ +[1] 7766 2348 │ │ │ │ │ │ │ │ │ │ $variables$`fishpond-package` │ │ │ │ │ -[1] 10305 2230 │ │ │ │ │ +[1] 10406 2242 │ │ │ │ │ │ │ │ │ │ $variables$getTrace │ │ │ │ │ -[1] 12816 1486 │ │ │ │ │ +[1] 12939 1499 │ │ │ │ │ │ │ │ │ │ $variables$importAllelicCounts │ │ │ │ │ -[1] 14592 5659 │ │ │ │ │ +[1] 14737 5672 │ │ │ │ │ │ │ │ │ │ $variables$isoformProportions │ │ │ │ │ -[1] 20539 1463 │ │ │ │ │ +[1] 20707 1475 │ │ │ │ │ │ │ │ │ │ $variables$labelKeep │ │ │ │ │ -[1] 22284 1753 │ │ │ │ │ +[1] 22474 1767 │ │ │ │ │ │ │ │ │ │ $variables$loadFry │ │ │ │ │ -[1] 24318 5868 │ │ │ │ │ +[1] 24531 5878 │ │ │ │ │ │ │ │ │ │ $variables$makeInfReps │ │ │ │ │ -[1] 30470 2180 │ │ │ │ │ +[1] 30702 2194 │ │ │ │ │ │ │ │ │ │ $variables$makeSimSwishData │ │ │ │ │ -[1] 32937 1852 │ │ │ │ │ +[1] 33194 1866 │ │ │ │ │ │ │ │ │ │ $variables$makeTx2Tss │ │ │ │ │ -[1] 35073 1507 │ │ │ │ │ +[1] 35353 1519 │ │ │ │ │ │ │ │ │ │ $variables$miniSwish │ │ │ │ │ -[1] 36860 2047 │ │ │ │ │ +[1] 37164 2059 │ │ │ │ │ │ │ │ │ │ $variables$plotAllelicGene │ │ │ │ │ -[1] 39193 5803 │ │ │ │ │ +[1] 39518 5815 │ │ │ │ │ │ │ │ │ │ $variables$plotAllelicHeatmap │ │ │ │ │ -[1] 45284 2140 │ │ │ │ │ +[1] 45630 2153 │ │ │ │ │ │ │ │ │ │ $variables$plotInfReps │ │ │ │ │ -[1] 47707 4704 │ │ │ │ │ +[1] 48075 4717 │ │ │ │ │ │ │ │ │ │ $variables$plotMASwish │ │ │ │ │ -[1] 52694 1230 │ │ │ │ │ +[1] 53085 1243 │ │ │ │ │ │ │ │ │ │ $variables$salmonEC │ │ │ │ │ -[1] 54205 2409 │ │ │ │ │ +[1] 54618 2421 │ │ │ │ │ │ │ │ │ │ $variables$scaleInfReps │ │ │ │ │ -[1] 56898 2676 │ │ │ │ │ +[1] 57332 2688 │ │ │ │ │ │ │ │ │ │ $variables$splitSwish │ │ │ │ │ -[1] 59855 2773 │ │ │ │ │ +[1] 60312 2784 │ │ │ │ │ │ │ │ │ │ $variables$swish │ │ │ │ │ -[1] 62906 7345 │ │ │ │ │ +[1] 63384 7355 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 286 │ │ │ │ │ +[1] 0 295 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 24037 281 │ │ │ │ │ +[1] 24241 290 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 30186 284 │ │ │ │ │ +[1] 30409 293 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 32650 287 │ │ │ │ │ +[1] 32896 298 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 34789 284 │ │ │ │ │ +[1] 35060 293 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 36580 280 │ │ │ │ │ +[1] 36872 292 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 38907 286 │ │ │ │ │ +[1] 39223 295 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 44996 288 │ │ │ │ │ +[1] 45333 297 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 47424 283 │ │ │ │ │ +[1] 47783 292 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 52411 283 │ │ │ │ │ +[1] 52792 293 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 53924 281 │ │ │ │ │ +[1] 54328 290 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1689 278 │ │ │ │ │ +[1] 1712 290 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 56614 284 │ │ │ │ │ +[1] 57039 293 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 59574 281 │ │ │ │ │ +[1] 60020 292 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 62628 278 │ │ │ │ │ +[1] 63096 288 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 4400 282 │ │ │ │ │ +[1] 4445 293 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 7408 278 │ │ │ │ │ +[1] 7477 289 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 10022 283 │ │ │ │ │ +[1] 10114 292 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 12535 281 │ │ │ │ │ +[1] 12648 291 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 14302 290 │ │ │ │ │ +[1] 14438 299 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 20251 288 │ │ │ │ │ +[1] 20409 298 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 22002 282 │ │ │ │ │ +[1] 22182 292 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/fishpond/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,24 +1,24 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-fishpond/man/addStatsFromCSV.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-fishpond/man/alevinEC.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-fishpond/man/computeInfRV.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-fishpond/man/deswish.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-fishpond/man/fishpond-package.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-fishpond/man/getTrace.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-fishpond/man/importAllelicCounts.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-fishpond/man/isoformProportions.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-fishpond/man/labelKeep.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-fishpond/man/loadFry.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-fishpond/man/makeInfReps.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-fishpond/man/makeSimSwishData.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-fishpond/man/makeTx2Tss.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-fishpond/man/miniSwish.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-fishpond/man/plotAllelicGene.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-fishpond/man/plotAllelicHeatmap.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-fishpond/man/plotInfReps.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-fishpond/man/plotMASwish.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-fishpond/man/salmonEC.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-fishpond/man/scaleInfReps.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-fishpond/man/splitSwish.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-fishpond/man/swish.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/addStatsFromCSV.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/alevinEC.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/computeInfRV.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/deswish.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/fishpond-package.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/getTrace.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/importAllelicCounts.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/isoformProportions.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/labelKeep.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/loadFry.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/makeInfReps.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/makeSimSwishData.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/makeTx2Tss.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/miniSwish.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotAllelicGene.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotAllelicHeatmap.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotInfReps.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/plotMASwish.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/salmonEC.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/scaleInfReps.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/splitSwish.Rd" │ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-fishpond-2.18.0+ds/man/swish.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 41 │ │ │ │ │ +[1] 56